Department of Physics and Astronomyhttp://hdl.handle.net/10211.2/1402
Physics and Astronomy Master's Thesis Collection | Faculty Publications and ResearchTue, 26 Sep 2017 21:53:47 GMT2017-09-26T21:53:47ZImplicit solvent calculations with explicit molecular models in amber with 3D-RISMhttp://hdl.handle.net/10211.3/196265
Implicit solvent calculations with explicit molecular models in amber with 3D-RISM
Luchko, Tyler
Sun, 01 Jan 2012 00:00:00 GMThttp://hdl.handle.net/10211.3/1962652012-01-01T00:00:00ZImplicit Solvent Models and Electrostatics in Molecular Recognitionhttp://hdl.handle.net/10211.3/196264
Implicit Solvent Models and Electrostatics in Molecular Recognition
Luchko, Tyler; Case, David A.
Sun, 01 Jan 2012 00:00:00 GMThttp://hdl.handle.net/10211.3/1962642012-01-01T00:00:00ZSmall molecule hydration energy and entropy from 3D-RISM.http://hdl.handle.net/10211.3/196248
Small molecule hydration energy and entropy from 3D-RISM.
Johnson, J.; Case, David A.; Yamazaki, T.; Gusarov, Sergey; Kovalenk, Andriy; Luchko, Tyler
Implicit solvent models offer an attractive way to estimate the effects of a solvent environment on the properties of small or large solutes without the complications of explicit simulations. One common test of accuracy is to compute the free energy of transfer from gas to liquid for a variety of small molecules, since many of these values have been measured. Studies of the temperature dependence of these values (i.e. solvation enthalpies and entropies) can provide additional insights into the performance of implicit solvent models. Here, we show how to compute temperature derivatives of hydration free energies for the 3D-RISM integral equation approach. We have computed hydration free energies of 1123 small drug-like molecules (both neutral and charged). Temperature derivatives were also used to calculate hydration energies and entropies of 74 of these molecules (both neutral and charged) for which experimental data is available. While direct results have rather poor agreement with experiment, we have found that several previously proposed linear hydration free energy correction schemes give good agreement with experiment. These corrections also provide good agreement for hydration energies and entropies though simple extensions are required in some cases.
Fri, 01 Jan 2016 00:00:00 GMThttp://hdl.handle.net/10211.3/1962482016-01-01T00:00:00ZCompetitive interaction of monovalent cations with DNA from 3D-RISMhttp://hdl.handle.net/10211.3/196249
Competitive interaction of monovalent cations with DNA from 3D-RISM
Giambaşu, George; Gebala, Magdalena; Panteva, Maria T.; Luchko, Tyler; Case, David A.; York, Darrin M.
The composition of the ion atmosphere surrounding nucleic acids affects their folding, condensation and binding to other molecules. It is thus of fundamental importance to gain predictive insight into the formation of the ion atmosphere and thermodynamic consequences when varying ionic conditions. An early step toward this goal is to benchmark computational models against quantitative experimental measurements. Herein, we test the ability of the three dimensional reference interaction site model (3D-RISM) to reproduce preferential interaction parameters determined from ion counting (IC) experiments for mixed alkali chlorides and dsDNA. Calculations agree well with experiment with slight deviations for salt concentrations >200 mM and capture the observed trend where the extent of cation accumulation around the DNA varies inversely with its ionic size. Ion distributions indicate that the smaller, more competitive cations accumulate to a greater extent near the phosphoryl groups, penetrating deeper into the grooves. In accord with experiment, calculated IC profiles do not vary with sequence, although the predicted ion distributions in the grooves are sequence and ion size dependent. Calculations on other nucleic acid conformations predict that the variation in linear charge density has a minor effect on the extent of cation competition.
Thu, 01 Jan 2015 00:00:00 GMThttp://hdl.handle.net/10211.3/1962492015-01-01T00:00:00Z